GeneHub-GEPIS: digital expression profiling for normal and cancer tissues based on an integrated gene database

Yan Zhang, Shiuh-Ming Luoh, Lawrence S. Hon, Robert Baertsch, William I. Wood, Zemin Zhang
2007 Nucleic Acids Research  
GeneHub-GEPIS is a web application that performs digital expression analysis in human and mouse tissues based on an integrated gene database. Using aggregated expressed sequence tag (EST) library information and EST counts, the application calculates the normalized gene expression levels across a large panel of normal and tumor tissues, thus providing rapid expression profiling for a given gene. The backend GeneHub component of the application contains pre-defined gene structures derived from
more » ... NA transcript sequences from major databases and includes extensive cross references for commonly used gene identifiers. ESTs are then linked to genes based on their precise genomic locations as determined by GMAP. This genome-based approach reduces incorrect matches between ESTs and genes, thus minimizing the noise seen with previous tools. In addition, the gene-centric design makes it possible to add several important features, including text searching capabilities, the ability to accept diverse input values, expression analysis for microRNAs, basic gene annotation, batch analysis, and linking between mouse and human genes. GeneHub-GEPIS is available at
doi:10.1093/nar/gkm381 pmid:17545196 pmcid:PMC1933245 fatcat:znnyvz2ez5aopb7aurvwkojygq